Citizen_Science_Environmental Monitoring_Pittcon_2017
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Open Source Instruments and Chemical Analysis Methods for a Citizen Science Based Environmental Monitoring Initiative. Presented at Pittcon 2017, Chicago, IL, March 7, 2017. Abstract link: https://webmobile.experientengage.com/%7EPIT171/#/eventItem/37877 check out AnalyzeChemicals.com for more information.
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The European MassBank server (www.massbank.eu) was founded in 2012 by the NORMAN Network (www.norman-network.net) to provide open access to mass spectra of substances of environmental interest contributed by NORMAN members. The automated workflow RMassBank was developed as a part of this effort (Stravs et al 2013, DOI: 10.1002/jms.3131; https://github.com/MassBank/RMassBank/). This workflow included automated processing of the mass spectral data, as well as automated annotation using the SMILES, Names and CAS numbers provided by the user. Cheminformatics toolkits (e.g. Open Babel, rcdk) and web services (e.g. the CACTUS Chemical Identifier Resolver, Chemical Translation Services (CTS), ChemSpider, PubChem) were then used to convert and/or retrieve the remaining information for completion of the MassBank records (additional names, InChIs, InChIKeys, several database identifiers, mol files), to avoid excessive burden on the users and reduce the chance of errors. To date, approximately 16,000 MS/MS spectra (61 %*) corresponding with 1,269 (18 %*) unique chemicals (*of all open data as of Nov. 2016) have been uploaded to MassBank.EU via RMassBank. Curating the MassBank.EU records, as part of efforts to provide EPA CompTox Dashboard identifiers (DTXSIDs) for each record, revealed several issues in data quality. In addition, the representation of “ambiguous substances”, for example complex surfactant mixtures of various chain lengths and branching or incompletely-defined structures of transformaton products, is an ongoing challenge. While “ambiguous structures” cannot be represented in the majority of cheminformatics tools, we report on proof-of-concept solutions in this work. This presentation reflects on the effectiveness of the original RMassBank concept but also identifies pitfalls that automated structure annotation with open resources offers to streamline spectra contributions from external laboratories and users with widely ranging cheminformatics experience. Note: this work does not necessarily reflect U.S. EPA policy.ICIC 2017: Looking at the gift horse: pros and cons of over 20 million patent...
Christopher Southan (The IUPHAR/BPS Guide to PHARMACOLOGY, UK)
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Environmental Cheminformatics for Unknown ID UC Davis Nov 2018
Environmental Cheminformatics to Identify Unknown Chemicals and their Effects
Assoc. Prof. Dr. Emma L. Schymanski
FNR ATTRACT Fellow and PI: Environmental Cheminformatics, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 avenue du Swing, L-4367 Belvaux, Luxembourg.
The Environmental Cheminformatics group at the Luxembourg Centre for Systems Biomedicine focuses on the comprehensive identification of known and unknown chemicals in our environment to investigate their effects on health and disease. The environment and the chemicals to which we are exposed is incredibly complex, with over 125 million chemicals registered in the largest chemical registry and over 70,000 in household use alone. Detectable molecules in complex samples can now be captured using high resolution mass spectrometry (HRMS), which provides a “snapshot” of all chemicals present in a sample and allows for retrospective data analysis through digital archiving. However, scientists cannot yet identify the vast majority of the tens of thousands of features in each sample, leading to critical bottlenecks in identification and data interpretation. For instance, recent studies indicate a strong connection between the gut microbiome and Parkinson’s disease, yet over 60 % of significant metabolites in microbiome experiments are unknown. Unknown identification remains extremely time consuming and, in many cases, a matter of luck. Prioritizing efforts to find significant metabolites or potentially toxic substances responsible for observed effects is the key, which involves reconciling highly complex samples with expert knowledge and careful validation. This talk will cover European, US and worldwide community initiatives to help connect knowledge on chemistry and toxicity with environmental observations - from compound databases to spectral libraries and retrospective screening. It will touch on the challenges of standardized structure representations, data curation, deposition and communication between resources. Finally, it will show how interdisciplinary efforts and data sharing can facilitate research in metabolomics, exposomics and beyond.
NOTE: some slides causing errors have been removed but can be accessed through the tinyurl on the front page.
Active hyperlinks can be retrieved using the tinyurl on the front page. Please cite this work if you use any of the contents.
Chemistry data delivery from the US-EPA to support environmental chemistry
Chemistry data delivery from the US-EPA to support environmental chemistryUS Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure
In recent years, the growth of scientific data and the increasing need for data sharing and collaboration in the field of environmental chemistry has led to the creation of various software and databases that facilitate research and development into the safety and toxicity of chemicals. The US-EPA Center for Computational Toxicology and Exposure has been developing software and databases that serve the chemistry community for many years. This presentation will focus on several web-based software applications which have been developed at the US-EPA and made available to the community. While the primary software application from the Center is the CompTox Chemicals Dashboard (https://comptox.epa.gov/dashboard), almost a dozen proof-of-concept applications have been built serving various capabilities. The publicly accessible Cheminformatics Modules (https://www.epa.gov/chemical-research/cheminformatics) provides access to six individual modules to allow for hazard comparison for sets of chemicals, structure-substructure-similarity searching, structure alerts and batch QSAR prediction of both physicochemical and toxicity endpoints. A number of other applications in development include a chemical transformations database and a database of analytical methods and open mass spectral data. Each of these depends on the underlying DSSTox chemicals database, a rich source of chemistry data for over 1.2 million chemical substances. To further extend the accessibility and usability of this vast repository, we have developed RESTful Public APIs hosted on the secure cloud.gov environment, enabling seamless integration of this rich data into computational biology pipelines and web visualizations. We will provide an overview of all tools in development, the integrated nature of the applications based on the underlying chemistry data, and the API which is now publicly available. This abstract does not necessarily represent the views or policies of the U.S. Environmental Protection Agency.Small molecule identification and the new MassBank
Since the beginning more than 10 years ago, the MassBank system
provided a user-friendly web interface. We now have improved
data access, version control and issue tracking by moving
the data to github, allowing for a whole new workflow
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Citizen_Science_Environmental Monitoring_Pittcon_2017
- 1. Open Source Instruments and Chemical Analysis Methods for a Citizen Science Based Environmental Monitoring Initiative Jay M. Patel, Mayank Patel Arno Bouwens Jamie Isidro Robert S Phillips PITTCON 2017 7th March, 2017 Chicago, IL www.AnalyzeChemicals.com
- 2. Outline ● Introduction – Citizen Science – Open Source Software (OSS) – Low Cost Microcomputers (LCM) – Open Source Hardware (OSH) ● ACH Instruments: Mod-Spec ● ACH Software: ChemAnalysis WorkBench ● ACH Methods ● Conclusions
- 3. 3 Citizen Science: History 1700s 1900 2005 April 2010 May 2010 2012 Charles Darwin Ben Franklin Christmas bird count ~60,000 participants in 2016 season BP oil spill Jeff Warren et al starts Public lab. $8000 raised for balloon kits $100,000+ raised through kickstarter 2014Yr 2017 Flint, MI Crisis 1800s ~1.5 million participants, 143 countries Kits for pH temp, DO, turbidity of water bodies MonitorWater.org PublicLab.org
- 4. 4 Open Source Software: History 1991 Apr 1995 2001 May 2002 2003 2008May 1995Yr
- 5. 5 Low Cost Microcomputers: History Uno, 16 MHz $24 2010 2012 Due, 84 MHz ~$50 2005 Rpi zero 1Ghz 512 MB RAM $5 2013 Model A 700 Mhz $25 Rpi 3 Model B 1.2 GHz, 1 GB RAM $35 Sept 2016, over 10 million sold Feb 2016 May 2016Yr
- 6. 6 Timeline for OSH Spectrometers Wheetrometer 1.0 Wheetrometer 2.0 Wheetrometer 3.0 (2014)2012 2013 2014 2015 Wheetrometer 3.0 Yr OSH: Open source Hardware RamanPi: 3D printed Raman running on RPi
- 7. 7 2012 2013 2014 2015Yr
- 8. Outline ● Introduction – Citizen Science – Open Source Software (OSS) – Low Cost Microcomputers (LCM) – Open Source Hardware (OSH) ● ACH Instruments: Mod-Spec ● ACH Software: ChemAnalysis WorkBench ● ACH Methods ● Conclusions
- 9. 9 ACH Instruments: Mod-Spec UV-VIS Exploded view of optical bench Overview of Mod- Spec Optics
- 10. 10 ChemAnalysis Workbench (CAW) ChemAnalysis Workbench Select Eclipse Strategic members Eclipse Science Group Steering Committee
- 11. 11 ACH Software: ChemAnalysis WorkBench
- 12. 12 Settings
- 13. 13 DExplore
- 14. 14 Perspectives
- 15. 15 CAW Tabs
- 16. 16 ACH Methods Database www.AnalyzeChemicals.com Contact us at support@analyzechemicals.com for contributing to ACH Methods Database
- 17. 17 Conclusions and Future Developments ● Mod-Spec UV-VIS is built on modular parts: – Can be easily modified to insert flow cells (for use as HPLC detectors), or high pressure cell. – Supports a large selection of CCD arrays from Hamamastu, Sony and Toshiba. ● ChemAnalysis Workbench is built on a java based eclipse platform: – Modular and extensible with plugins – Further work include support for HPLC pumps, fluorescence, CE and potentiostat perspectives . ● ACH methods is an open source, crowdsourced alternative to proprietary products like CAS/Scifinder's MethodNow: – Includes methods and related experimental data for wide type of chemicals such as pesticides, pharmaceuticals, heavy metals etc.
- 18. 18 Acknowledgments ● David Brunell ● Ben Hickman ● UGA instrument shop ● Joel Koenka ● ACH volunteers
- 19. 19 Thank You Questions? Jay M. Patel Patel.Jay@AnalyzeChemicals.com www.AnalyzeChemicals.com Support@AnalyzeChemicals.com